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Package 116/294HostnameOS / ArchBUILDCHECKBUILD BIN
GLAD 1.18.0
Philippe Hupe
Bioconductor Changelog
Snapshot Date: 2009-04-18 11:27:48 -0700 (Sat, 18 Apr 2009)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_3/madman/Rpacks/GLAD
Last Changed Rev: 34811 / Revision: 38965
Last Changed Date: 2008-10-21 15:32:58 -0700 (Tue, 21 Oct 2008)
wilson2 Linux (openSUSE 11.1) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
pitt Mac OS X Tiger (10.4.11) / i386  OK  OK  OK 
pelham Mac OS X Leopard (10.5.6) / i386  OK [ OK ] OK 
Package: GLAD
Version: 1.18.0
Command: /Library/Frameworks/R.framework/Versions/2.8/Resources/bin/R CMD check --no-vignettes GLAD_1.18.0.tar.gz
StartedAt: 2009-04-18 17:30:29 -0700 (Sat, 18 Apr 2009)
EndedAt: 2009-04-18 17:31:10 -0700 (Sat, 18 Apr 2009)
EllapsedTime: 41.9 seconds
RetCode: 0
Status: OK
CheckDir: GLAD.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.3-bioc/meat/GLAD.Rcheck'
* using R version 2.8.1 Patched (2009-03-18 r48200)
* using session charset: ASCII
* checking for file 'GLAD/DESCRIPTION' ... OK
* this is package 'GLAD' version '1.18.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'GLAD' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
chrBreakpoints.profileCGH: no visible global function definition for
  'laws'
chrBreakpoints.profileCGH: possible error in aws(y =
  subsetdata$LogRatio, x = x, hinit = hinit, hmax = hmax, sigma2 =
  sigma, NN = FALSE, symmetric = TRUE, ...): unused argument(s) (x = x,
  hinit = hinit, NN = FALSE, symmetric = TRUE)
chrBreakpoints.profileCGH: possible error in aws(y =
  subsetdata$LogRatio, hinit = hinit, hmax = hmax, sigma2 = sigma,
  symmetric = TRUE, ...): unused argument(s) (hinit = hinit, symmetric
  = TRUE)
plotProfile.profileCGH: no visible binding for global variable
  'cytoband'
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking data for non-ASCII characters ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating GLAD-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating GLAD-manual.tex ... OK
* checking GLAD-manual.tex using pdflatex ... OK

GLAD.Rcheck/00install.out:

* Installing *source* package 'GLAD' ...

Configuring variable environment

OS is: Darwin
src/Makevars has been created
PKG_CFLAGS+=-DIS_MAC_OS
PKG_CXXFLAGS+=-DIS_MAC_OS
variable environment completed

** libs
** arch - i386
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386  -I/usr/local/include   -DIS_MAC_OS -fPIC  -g -O2 -Wall -c distance.c -o distance.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386  -I/usr/local/include   -DIS_MAC_OS -fPIC  -g -O2 -Wall -c glad-function.c -o glad-function.o
g++-4.0 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386  -I/usr/local/include   -DIS_MAC_OS -fPIC  -g -O2 -Wall -fasm-blocks -c glad.cpp -o glad.o
glad.cpp: In function 'void detectOutliers(double*, int*, int*, int*, int*, int*, double*, int*)':
glad.cpp:112: warning: comparison between signed and unsigned integer expressions
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386  -I/usr/local/include   -DIS_MAC_OS -fPIC  -g -O2 -Wall -c hclust.c -o hclust.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386  -I/usr/local/include   -DIS_MAC_OS -fPIC  -g -O2 -Wall -c laws.c -o laws.o
g++-4.2 -arch i386 -dynamiclib -Wl,-headerpad_max_install_names  -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o GLAD.so distance.o glad-function.o glad.o hclust.o laws.o   -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** R
** data
** demo
** inst
** preparing package for lazy loading
** help
 >>> Building/Updating help pages for package 'GLAD'
     Formats: text html latex example 
  ChrNumeric                        text    html    latex   example
  ColorBar                          text    html    latex   example
  GLAD-internal                     text    html    latex
  arrayCGH                          text    html    latex   example
  arrayPersp                        text    html    latex   example
  arrayPlot                         text    html    latex   example
  as.data.frame.profileCGH          text    html    latex   example
  as.profileCGH                     text    html    latex   example
  bladder                           text    html    latex   example
  cytoband                          text    html    latex   example
  daglad                            text    html    latex   example
  glad                              text    html    latex   example
  hclust                            text    html    latex   example
  kernel                            text    html    latex
  myPalette                         text    html    latex   example
  plotProfile                       text    html    latex   example
  profileCGH                        text    html    latex   example
  snijders                          text    html    latex   example
  tkdaglad                          text    html    latex   example
  veltman                           text    html    latex   example
** building package indices ...
* DONE (GLAD)